To solve the difficulty in correlating marine vessel tracks in the overlapping monitoring area of multiple radars when the radar has a system error, a method of correlation based on topological polygons is proposed in this study. One track from each radar was selected to calculate the correlation at each time point. First, the surrounding targets of the two tracks were filtered and a matching algorithm was used to keep the number of surrounding targets consistent. Second, topological polygons were constructed and a similarity function was constructed to calculate the similarity of the topological polygons as the correlation value of the two tracks to be correlated. Finally, the mean value of the correlation degree at each moment was calculated and compared with a threshold value to determine whether the tracks were correlated. In the simulation experiment, the correct mean rate of the method in this study was 90.87%, and its performance was better than that of the comparison algorithm in a variety of scenarios, such as radar missed detection. This method provides an effective and practical way to realize the track correlation of marine vessels under the condition of radar system error.